J'ai suivi toutes les instructions sur https://github.com/Rdatatable/data.table/wiki/Installation et recherché StackOverflow, mais je n'arrive pas à installer data.table à partir de la source (pour la prise en charge d'OpenMP) sur Mac 10.14.6 avec R4.0. J'obtiens toujours cette erreur lorsque j'essaie d'installer à partir des sources :
> install.packages("data.table", type="source", Ncpus = 7)
trying URL 'https://cran.us.r-project.org/src/contrib/data.table_1.12.8.tar.gz'
Content type 'application/octet-stream' length 4948391 bytes (4.7 MB)
==================================================
downloaded 4.7 MB
* installing *source* package âdata.tableâ ...
** package âdata.tableâ successfully unpacked and MD5 sums checked
** using staged installation
zlib 1.2.11 is available ok
** libs
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c assign.c -o assign.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c between.c -o between.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c bmerge.c -o bmerge.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c chmatch.c -o chmatch.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c cj.c -o cj.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c coalesce.c -o coalesce.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c dogroups.c -o dogroups.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fastmean.c -o fastmean.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fcast.c -o fcast.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fifelse.c -o fifelse.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fmelt.c -o fmelt.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c forder.c -o forder.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frank.c -o frank.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fread.c -o fread.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c freadR.c -o freadR.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c froll.c -o froll.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frollR.c -o frollR.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frolladaptive.c -o frolladaptive.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fsort.c -o fsort.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwrite.c -o fwrite.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwriteR.c -o fwriteR.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c gsumm.c -o gsumm.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c ijoin.c -o ijoin.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c inrange.c -o inrange.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nafill.c -o nafill.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nqrecreateindices.c -o nqrecreateindices.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c openmp-utils.c -o openmp-utils.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c quickselect.c -o quickselect.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c rbindlist.c -o rbindlist.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c reorder.c -o reorder.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c shift.c -o shift.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c subset.c -o subset.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c transpose.c -o transpose.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c types.c -o types.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c uniqlist.c -o uniqlist.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c utils.c -o utils.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c vecseq.c -o vecseq.o
/usr/local/opt/llvm/bin/clang -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c wrappers.c -o wrappers.o
/usr/local/opt/llvm/bin/clang -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -lz -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
ld: unknown option: -platform_version
clang-10: error: linker command failed with exit code 1 (use -v to see invocation)
make: *** [data.table.so] Error 1
ERROR: compilation failed for package âdata.tableâ
* removing â/Library/Frameworks/R.framework/Versions/4.0/Resources/library/data.tableâ
Warning in install.packages :
installation of package âdata.tableâ had non-zero exit status
The downloaded source packages are in
â/private/var/folders/fs/7z2xwjxx0vn3kj7x7khc06980000gp/T/RtmpyDidEl/downloaded_packagesâ
> sessionInfo()
R version 4.0.0 (2020-04-24)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.0/Resources/lib/libRlapack.dylib
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] compiler_4.0.0 tools_4.0.0 packrat_0.5.0
Pouvez-vous essayer gcc au lieu de clang ?
Je viens de le voir récemment
https://github.com/su/R-mac-dev
Je ne l'ai pas regardĂ© car je n'ai pas de mac, mais peut-ĂȘtre que cela sera utile
Désolé, je suis un peu novice en la matiÚre. Comment pourrais-je utiliser gcc à la place ?
Peu importe. Je l'ai compris et je suis capable d'installer avec un support multithread. J'ai dĂ» changer mon fichier .R/Makevars
. Voici les nouveaux contenus :
LDFLAGS= -L/usr/local/clang4/lib
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/gfortran/bin/g++
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++
LLVM_LOC = /usr/local/opt/llvm
CC=/usr/local/gfortran/bin/gcc -fopenmp
CXX=/usr/local/gfortran/bin/g++ -fopenmp
# -O3 should be faster than -O2 (default) level optimisation ..
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
@ jrf1111 merci d'avoir fourni la solution, fermeture puis
DĂ©solĂ© de dĂ©ranger mais j'essaye de dĂ©chiffrer la solution car j'ai le mĂȘme problĂšme (oui, dĂ©butant)
De quelle maniĂšre avoir llvm et utiliser d'autres compilateurs C (pas ceux de llvm, qui me donnent Ă©galement cette Ă©trange erreur dans le premier message) rĂ©sout le problĂšme ? Au cas oĂč je n'aurais pas ce gfortran, mais j'ai en fait suivi toutes les instructions https://github.com/Rdatatable/data.table/wiki/Installation#openmp -enabled-compiler-for-mac mais avec une installation manuelle, quoi dois-je Ă©crire dans Makevars pour que data.table s'exĂ©cute en multithread ?
Je suis passé à gfortran par https://mac.r-project.org/tools/ , https://cran.r-project.org/bin/macosx/tools/ , configurez .R/Makevars
comme ceci
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin18/8.2.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=/usr/local/gfortran/bin/gcc
CXX=/usr/local/gfortran/bin/g++
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++
LLVM_LOC = /usr/local/gfortran
CC=$(LLVM_LOC)/bin/gcc -fopenmp
CXX=$(LLVM_LOC)/bin/g++ -fopenmp
# -O3 should be faster than -O2 (default) level optimisation ..
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
et maintenant, pendant que j'essaie d'installer la version développeur à partir du référentiel, j'obtiens
data.table::update.dev.pkg()
Warning: unable to access index for repository https://Rdatatable.gitlab.io/data.table/bin/macosx/contrib/4.0:
cannot open URL 'https://Rdatatable.gitlab.io/data.table/bin/macosx/contrib/4.0/PACKAGES'
Package which is only available in source form, and may need compilation of C/C++/Fortran:
âdata.tableâ
Do you want to attempt to install these from sources? (Yes/no/cancel) Yes
installing the source package âdata.tableâ
trying URL 'https://Rdatatable.gitlab.io/data.table/src/contrib/data.table_1.12.9.tar.gz'
Content type 'application/gzip' length 5195275 bytes (5.0 MB)
downloaded 5.0 MB
installing source package âdata.tableâ ...
** using staged installation
*** pkg-config is not installed.
*** Compilation will now be attempted and if it works you can ignore this message. However,
*** if compilation fails, try 'locate zlib.h zconf.h' and ensure the zlib development library
*** is installed :
*** deb: zlib1g-dev (Debian, Ubuntu, ...)
*** rpm: zlib-devel (Fedora, EPEL, ...)
*** brew: zlib (OSX)
*** Note that zlib is required to compile R itself so you may find the advice in the R-admin
*** guide helpful regarding zlib. On Debian/Ubuntu, zlib1g-dev is a dependency of r-base as
*** shown by 'apt-cache showsrc r-base | grep ^Build-Depends | grep zlib', and therefore
*** 'sudo apt-get build-dep r-base' should be sufficient too.
*** To silence this message, please ensure that :
*** 1) 'pkg-config --exists zlib' succeeds (i.e. $? -eq 0)
*** 2) 'pkg-config --libs zlib' contains -lz
*** Compilation will now be attempted ...
** libs
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c assign.c -o assign.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c between.c -o between.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c bmerge.c -o bmerge.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c chmatch.c -o chmatch.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c cj.c -o cj.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c coalesce.c -o coalesce.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c dogroups.c -o dogroups.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fastmean.c -o fastmean.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fcast.c -o fcast.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fifelse.c -o fifelse.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fmelt.c -o fmelt.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c forder.c -o forder.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frank.c -o frank.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fread.c -o fread.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c freadR.c -o freadR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c froll.c -o froll.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frollR.c -o frollR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frolladaptive.c -o frolladaptive.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fsort.c -o fsort.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwrite.c -o fwrite.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwriteR.c -o fwriteR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c gsumm.c -o gsumm.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c ijoin.c -o ijoin.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c inrange.c -o inrange.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nafill.c -o nafill.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nqrecreateindices.c -o nqrecreateindices.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c openmp-utils.c -o openmp-utils.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c quickselect.c -o quickselect.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c rbindlist.c -o rbindlist.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c reorder.c -o reorder.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c shift.c -o shift.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c subset.c -o subset.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c transpose.c -o transpose.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c types.c -o types.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c uniqlist.c -o uniqlist.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c utils.c -o utils.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c vecseq.c -o vecseq.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/gfortran/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c wrappers.c -o wrappers.o
/usr/local/gfortran/bin/gcc -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/gfortran/lib -Wl,-rpath,/usr/local/gfortran/lib -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Library/Frameworks/R.framework/Versions/4.0/Resources/library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
Error: package or namespace load failed for âdata.tableâ in library.dynam(lib, package, package.lib):
shared object âdatatable.soâ not found
Error: loading failed
Execution halted
ERROR: loading failed
removing â/Library/Frameworks/R.framework/Versions/4.0/Resources/library/data.tableâ
restoring previous â/Library/Frameworks/R.framework/Versions/4.0/Resources/library/data.tableâ
The downloaded source packages are in
â/private/var/folders/z7/r94g4j6j4z33r99np7kwns2nwz14jw/T/RtmppDABFK/downloaded_packagesâ
R data.table package has been updated to NA (1.12.8)
Warning message:
In utils::install.packages(pkg, repos = repo, type = type, lib = lib, :
installation of package âdata.tableâ had non-zero exit status
La version CRAN fonctionne mais avec un seul thread. Il existe un fil de discussion stackoverflow à ce sujet https://stackoverflow.com/questions/59658131/error-package-or-namespace-load-failed-for-data-table-in-library-dynamlib-p qui ne fournit aucune réponse utile.
Vous devrez peut-ĂȘtre utiliser la version 6.3.0 de gfortran disponible ici : https://github.com/fxcoudert/gfortran-for-macOS/releases/tag/6.3
Assurez-vous Ă©galement de mettre Ă jour votre fichier Makevars.
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
Malheureusement non. Le problĂšme persiste avec gfortran 6.3.0 et 8.2.0
Avez-vous supprimé l'installation précédente de data.table ? Et avez-vous installé la version CRAN au lieu de la version développeur ?
Oui, j'en ai bien sĂ»r. J'ai essayĂ© avec tous et mĂȘme rĂ©sultat : l'erreur avec la version dĂ©veloppeur, une installation rĂ©ussie mais un seul thread avec CRAN (Merci d'avoir essayĂ© de m'aider !)
Il semble qu'il y ait encore quelques différences entre votre fichier Makevars et le mien. Essayez simplement de remplacer l'intégralité de votre fichier Makevars par ce que j'ai utilisé :
LDFLAGS= -L/usr/local/clang4/lib
FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm
CC=/usr/local/clang4/bin/clang
CXX=/usr/local/gfortran/bin/g++
CXX1X=/usr/local/gfortran/bin/g++
CXX98=/usr/local/gfortran/bin/g++
CXX11=/usr/local/gfortran/bin/g++
CXX14=/usr/local/gfortran/bin/g++
CXX17=/usr/local/gfortran/bin/g++
LLVM_LOC = /usr/local/opt/llvm
CC=/usr/local/gfortran/bin/gcc -fopenmp
CXX=/usr/local/gfortran/bin/g++ -fopenmp
# -O3 should be faster than -O2 (default) level optimisation ..
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
redémarré, suivi vos conseils, cela fonctionne maintenant. Merci!!!
Heureux d'avoir pu aider!
Suite aux suggestions ci-dessus, j'ai eu les erreurs suivantes
[1] "en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8"
Erreur : le chargement du package ou de l'espace de noms a échoué pour 'data.table' dans library.dynam(lib, package, package.lib) :
objet partagé 'datatable.so' introuvable
Erreur : échec du chargement
Exécution interrompue
ERREURÂ : Ă©chec du chargement
Aucune suggestion?
@likanzhan semble ĂȘtre un problĂšme diffĂ©rent alors, veuillez crĂ©er un nouveau problĂšme et mettre toutes les entrĂ©es et sorties de la tentative d'installation dans la session R nouvellement dĂ©marrĂ©e.
@jangorecki
install.packages("data.table", type = "source", repos = "https://Rdatatable.gitlab.io/data.table")
Installing package into â/Users/lzhan/Râ
(as âlibâ is unspecified)
trying URL 'https://Rdatatable.gitlab.io/data.table/src/contrib/data.table_1.12.9.tar.gz'
Content type 'application/gzip' length 5195275 bytes (5.0 MB)
downloaded 5.0 MB
[1] "en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8"
* installing *source* package âdata.tableâ ...
** using staged installation
*** pkg-config is not installed.
*** Compilation will now be attempted and if it works you can ignore this message. However,
*** if compilation fails, try 'locate zlib.h zconf.h' and ensure the zlib development library
*** is installed :
*** deb: zlib1g-dev (Debian, Ubuntu, ...)
*** rpm: zlib-devel (Fedora, EPEL, ...)
*** brew: zlib (OSX)
*** Note that zlib is required to compile R itself so you may find the advice in the R-admin
*** guide helpful regarding zlib. On Debian/Ubuntu, zlib1g-dev is a dependency of r-base as
*** shown by 'apt-cache showsrc r-base | grep ^Build-Depends | grep zlib', and therefore
*** 'sudo apt-get build-dep r-base' should be sufficient too.
*** To silence this message, please ensure that :
*** 1) 'pkg-config --exists zlib' succeeds (i.e. $? -eq 0)
*** 2) 'pkg-config --libs zlib' contains -lz
*** Compilation will now be attempted ...
** libs
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c assign.c -o assign.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c between.c -o between.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c bmerge.c -o bmerge.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c chmatch.c -o chmatch.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c cj.c -o cj.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c coalesce.c -o coalesce.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c dogroups.c -o dogroups.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fastmean.c -o fastmean.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fcast.c -o fcast.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fifelse.c -o fifelse.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fmelt.c -o fmelt.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c forder.c -o forder.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frank.c -o frank.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fread.c -o fread.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c freadR.c -o freadR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c froll.c -o froll.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frollR.c -o frollR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c frolladaptive.c -o frolladaptive.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fsort.c -o fsort.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwrite.c -o fwrite.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c fwriteR.c -o fwriteR.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c gsumm.c -o gsumm.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c ijoin.c -o ijoin.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c init.c -o init.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c inrange.c -o inrange.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nafill.c -o nafill.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c nqrecreateindices.c -o nqrecreateindices.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c openmp-utils.c -o openmp-utils.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c quickselect.c -o quickselect.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c rbindlist.c -o rbindlist.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c reorder.c -o reorder.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c shift.c -o shift.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c subset.c -o subset.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c transpose.c -o transpose.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c types.c -o types.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c uniqlist.c -o uniqlist.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c utils.c -o utils.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c vecseq.c -o vecseq.o
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c wrappers.c -o wrappers.o
/usr/local/gfortran/bin/gcc -fopenmp -dynamiclib -Wl,-headerpad_max_install_names -undefined dynamic_lookup -single_module -multiply_defined suppress -L/Library/Frameworks/R.framework/Resources/lib -L/usr/local/opt/gettext/lib -L/usr/local/opt/llvm/lib -Wl,-rpath,/usr/local/opt/llvm/lib -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -F/Library/Frameworks/R.framework/.. -framework R -Wl,-framework -Wl,CoreFoundation
installing to /Users/lzhan/R/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
[1] "en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8"
** help
*** installing help indices
** building package indices
[1] "en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8"
** installing vignettes
** testing if installed package can be loaded from temporary location
[1] "en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8"
Error: package or namespace load failed for âdata.tableâ in library.dynam(lib, package, package.lib):
shared object âdatatable.soâ not found
Error: loading failed
Execution halted
ERROR: loading failed
* removing â/Users/lzhan/R/data.tableâ
The downloaded source packages are in
â/private/var/folders/qz/0srg88cd2459h1cbn623wrt00000gq/T/Rtmpgzby8h/downloaded_packagesâ
Warning message:
In install.packages("data.table", type = "source", repos = "https://Rdatatable.gitlab.io/data.table") :
installation of package âdata.tableâ had non-zero exit status
Merci !
La solution ci-dessous a fonctionné pour moi:
Peu importe. Je l'ai compris et je suis capable d'installer avec un support multithread. J'ai dĂ» changer mon fichier
.R/Makevars
. Voici les nouveaux contenus :LDFLAGS= -L/usr/local/clang4/lib FLIBS=-L/usr/local/gfortran/lib/gcc/x86_64-apple-darwin16/6.3.0 -L/usr/local/gfortran/lib -lgfortran -lquadmath -lm CC=/usr/local/clang4/bin/clang CXX=/usr/local/gfortran/bin/g++ CXX1X=/usr/local/gfortran/bin/g++ CXX98=/usr/local/gfortran/bin/g++ CXX11=/usr/local/gfortran/bin/g++ CXX14=/usr/local/gfortran/bin/g++ CXX17=/usr/local/gfortran/bin/g++ LLVM_LOC = /usr/local/opt/llvm CC=/usr/local/gfortran/bin/gcc -fopenmp CXX=/usr/local/gfortran/bin/g++ -fopenmp # -O3 should be faster than -O2 (default) level optimisation .. CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/lib CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include
@jangorecki Il serait utile de mettre Ă jour le fichier Makevars sur le wiki d'installation -- merci Ă vous et Ă l'Ă©quipe Rdatatable !
Pour ce qui compte, j'ai dû réinstaller à partir de zéro pour Catalina. J'ai découvert que llvm ne fonctionne toujours pas, alors que définir les .Makevars avec les compilateurs gfortran (comme ci-dessus, mais aussi pour la version 8.2.0) fait l'affaire.
Jamais réussi à terminer la compilation avec llvm, à la fois à Mojave et à Catalina.
J'ai également ce problÚme, en utilisant à la fois le fichier .R/Makevars suggéré sur la page readme (qui signale l'erreur standard au bas de cette page et m'a conduit ici) et avec le code de @daynefiler ci-dessus. Cela génÚre cette sortie :
> install.packages("data.table", type = "source",
+ repos = "https://Rdatatable.gitlab.io/data.table")
trying URL 'https://Rdatatable.gitlab.io/data.table/src/contrib/data.table_1.12.9.tar.gz'
Content type 'application/gzip' length 5208337 bytes (5.0 MB)
==================================================
downloaded 5.0 MB
* installing *source* package âdata.tableâ ...
** using staged installation
*** pkg-config is not installed.
*** Compilation will now be attempted and if it works you can ignore this message. However,
*** if compilation fails, try 'locate zlib.h zconf.h' and ensure the zlib development library
*** is installed :
*** deb: zlib1g-dev (Debian, Ubuntu, ...)
*** rpm: zlib-devel (Fedora, EPEL, ...)
*** brew: zlib (OSX)
*** Note that zlib is required to compile R itself so you may find the advice in the R-admin
*** guide helpful regarding zlib. On Debian/Ubuntu, zlib1g-dev is a dependency of r-base as
*** shown by 'apt-cache showsrc r-base | grep ^Build-Depends | grep zlib', and therefore
*** 'sudo apt-get build-dep r-base' should be sufficient too.
*** To silence this message, please ensure that :
*** 1) 'pkg-config --exists zlib' succeeds (i.e. $? -eq 0)
*** 2) 'pkg-config --libs zlib' contains -lz
*** Compilation will now be attempted ...
** libs
/usr/local/gfortran/bin/gcc -fopenmp -I"/Library/Frameworks/R.framework/Resources/include" -DNDEBUG -I/usr/local/opt/gettext/include -I/usr/local/opt/llvm/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -fPIC -g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe -c assign.c -o assign.o
/bin/sh: /usr/local/gfortran/bin/gcc: No such file or directory
make: *** [assign.o] Error 127
ERROR: compilation failed for package âdata.tableâ
* removing â/Library/Frameworks/R.framework/Versions/4.0/Resources/library/data.tableâ
Warning in install.packages :
installation of package âdata.tableâ had non-zero exit status
The downloaded source packages are in
â/private/var/folders/8n/wm3qzjnn2dx4l_lznyk0fthr00_bd1/T/Rtmp1SObio/downloaded_packagesâ
L'installation Ă l'aide de l'habituel install.packages("data.table") fonctionne, mais entraĂźne le problĂšme multicĆur que ce correctif essaie de rĂ©soudre
@FarMar pourriez-vous vérifier si install.packages("data.table", type="source")
fonctionne pour vous ? On dirait que votre compilateur est mal défini dans Makevars.
@jangorecki Cela fonctionne avec le fichier Makevar supprimé, mais renvoie le "pas d'erreur OpenMP", identique au référentiel CRAN. Il échoue avec le fichier Makevars détaillé par @jrf1111 et dans les réponses de @daynefiler ci-dessus
@FarMar Avant d'essayer de compiler data.table avec des Makevars personnalisés, assurez-vous qu'il compile quoi que ce soit. Par quoi que ce soit, j'entends un package avec du code compilé. Sinon, le problÚme n'est pas vraiment lié au code data.table. Une fois que votre compilateur peut compiler n'importe quoi, il peut y avoir un problÚme data.table lorsque la compilation échoue.
Si vous voulez suivre le chemin de ce fil, vous devrez probablement installer un logiciel manquant ou configurer des chemins, donc Makevars à partir d'ici spécifiera correctement le compilateur.
Sinon, vous pouvez revenir au point oĂč votre compilateur fonctionne, puis essayez de suivre https://github.com/Rdatatable/data.table/wiki/Installation wiki, puis en cas d'Ă©chec, ouvrez un nouveau problĂšme avec vos Makevars et la sortie .
Dans les deux cas, vous devez vous assurer que la compilation fonctionne sur n'importe quoi.
Pour vĂ©rifier que vous pouvez essayer d'installer n'importe quel package avec du code compilĂ©. J'ai un paquet de jouets "hello world from C" qui devrait ĂȘtre suffisant
install.packages("r.gitlab.ci", repos="https://jangorecki.gitlab.io/r.gitlab.ci")
lors de l'installation du package Ă partir de CRAN, vous devez ajouter type="source"
car CRAN a des binaires mac, qui seront utilisés par défaut, plutÎt que des sources de package.
@FarMar notez cette ligne de la sortie de votre installation
/usr/local/gfortran/bin/gcc : aucun fichier ou répertoire de ce type
Cela signifie que votre machine est configurée pour rechercher gcc
sur ce chemin : /usr/local/gfortran/bin/gcc
Vous pouvez vérifier si ce fichier existe sur votre machine. J'ai gcc
là -bas sur Mac (mais malheureusement, je ne sais pas exactement comment il est arrivé là , j'espÚre le wiki d'installation).
Personnellement, j'utilise llvm
sur Mac Ă /usr/local/opt/llvm
que j'ai configuré à partir du wiki d'installation.
Dans les deux cas, il doit ĂȘtre dĂ©fini comme CC
dans votre ~/.R/Makevars
.
J'espĂšre que cela pourra aider.
Sinon, vous pouvez revenir au point oĂč votre compilateur fonctionne, puis essayez de suivre https://github.com/Rdatatable/data.table/wiki/Installation wiki, puis en cas d'Ă©chec, ouvrez un nouveau problĂšme avec vos Makevars et la sortie .
@jangorecki, je vais Markevars
dans votre fichier readme. Je n'ai pas pu compiler votre test avec le Makevars
, ça marche bien sans.
bonjour Ă tous -- merci pour ce fil ! J'ai suivi les instructions d'installation de macOS Ă l' aide d'une llvm
partir de brew, mais je n'ai pas pu installer ce package avec
install.packages("data.table", type = "source", repos = "https://Rdatatable.gitlab.io/data.table")
la compilation a toujours échoué avec cette erreur :
Error: package or namespace load failed for âdata.tableâ in library.dynam(lib, package, package.lib):
shared object âdatatable.soâ not found
aprÚs quelques headbanging sur mon clavier, j'ai trouvé que cet avertissement s'est avéré trÚs utile :
** using staged installation
*** pkg-config is not installed.
*** Compilation will now be attempted and if it works you can ignore this message. However,
*** if compilation fails, try 'locate zlib.h zconf.h' and ensure the zlib development library
*** is installed :
*** deb: zlib1g-dev (Debian, Ubuntu, ...)
*** rpm: zlib-devel (Fedora, EPEL, ...)
*** brew: zlib (OSX)
*** Note that zlib is required to compile R itself so you may find the advice in the R-admin
*** guide helpful regarding zlib. On Debian/Ubuntu, zlib1g-dev is a dependency of r-base as
*** shown by 'apt-cache showsrc r-base | grep ^Build-Depends | grep zlib', and therefore
*** 'sudo apt-get build-dep r-base' should be sufficient too.
*** To silence this message, please ensure that :
*** 1) 'pkg-config --exists zlib' succeeds (i.e. $? -eq 0)
*** 2) 'pkg-config --libs zlib' contains -lz
*** Compilation will now be attempted ...
dans mon cas, locate
n'a pas fonctionné. J'ai essayé locate zlib.h zconf.h
et j'ai
WARNING: The locate database (/var/db/locate.database) does not exist.
To create the database, run the following command:
sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.locate.plist
ma machine est presque neuve, c'est peut-ĂȘtre pour ça que j'ai ce message. en tout cas, j'ai exĂ©cutĂ© cette commande launchctl load
et j'ai attendu quelques minutes, aprĂšs quoi locate
pouvaient trouver plusieurs endroits oĂč zlib.h
et zconf.h
trouvaient sur mon systÚme. avec cela en place, une installation source a fonctionné à merveille.
RĂSUMĂ : peut-ĂȘtre exagĂ©rĂ©, mais ce qui a fonctionnĂ© pour moi, c'est d'effectuer ces brew
installations avant d'installer data.table
partir de la source :
brew update
brew install llvm pkg-config zlib gettext
puis construisez la base de données pour locate
:
sudo launchctl load -w /System/Library/LaunchDaemons/com.apple.locate.plist
et utilisez le fichier ~/.R/Makevars
de la page d'installation avec un indicateur de compilateur C++ supplémentaire pour zlib
:
LLVM_LOC = /usr/local/opt/llvm
CC=$(LLVM_LOC)/bin/clang -fopenmp
CXX=$(LLVM_LOC)/bin/clang++ -fopenmp
# -O3 should be faster than -O2 (default) level optimisation ..
CFLAGS=-g -O3 -Wall -pedantic -std=gnu99 -mtune=native -pipe
CXXFLAGS=-g -O3 -Wall -pedantic -std=c++11 -mtune=native -pipe
LDFLAGS=-L/usr/local/opt/gettext/lib -L$(LLVM_LOC)/lib -Wl,-rpath,$(LLVM_LOC)/libi -L/usr/local/opt/zlib/lib
CPPFLAGS=-I/usr/local/opt/gettext/include -I$(LLVM_LOC)/include -I/Library/Developer/CommandLineTools/SDKs/MacOSX.sdk/usr/include -I/usr/local/opt/zlib/include
j'espĂšre que cela peut sauver quelqu'un de futurs maux de tĂȘte !
Commentaire le plus utile
Peu importe. Je l'ai compris et je suis capable d'installer avec un support multithread. J'ai dĂ» changer mon fichier
.R/Makevars
. Voici les nouveaux contenus :